Cambodia went up within seven minutes through a controversial goal by Chan Vathanaka at the match in Myanmar's commercial capital Yangon.
The Cambodian was called offside by the linesman but the referee allowed play to continue, judging the through ball had come off a Malaysian player.
The 2010 champion's defence could only look on as Vathanaka dribbled around the keeper and easily slotted the ball home.
Malaysia's Syazwan Zainon puts his team back in the game shortly before half-time but Cambodia's Vathanka struck once more after the break.
It was left to rising star Yahya to save the day.
He comfortably slotted home a Hazwan Bakri cross in the 69th minute and followed up eleven minutes later with a second successful strike.
Myanmar, co-hosts of this year's tournament alongside the Philippines, lost at home on Sunday to Vietnam 2-1.